The Anti-Corruption Bureau of Ukraine (NABU) did not identify the two officials but said the fraud had cost the budget 149 million hryvnias (USD 5.6 million in today's exchange rate) in 2016.
The bureau said the arrangement involved an oil purchase contract that was later revised to inflate the original price by 16 per cent to benefit the unnamed supplier.
"NABU detectives and special anti-corruption prosecutors have detained two suspected culprits -- a deputy defence minister of Ukraine and the director of the state resource procurement and supply department of the Ukrainian defence ministry," NABU said in a statement.
Corruption has long ravaged the crisis-torn former Soviet republic and been a top concern of both Ukraine's foreign partners and global financial support organisations such as the International Monetary Fund (IMF).
But NABU has faced stiff resistance since its launch in December 2015 from institutions such as the general prosecutor's office and the Security Service of Ukraine (SBU).
Analysts view both as controlled by vested interests and incapable of leading independent probes into financial misdeeds.
The IMF is pressing the pro-Western leaders who rose to power after a 2014 revolution that ousted a Russian-backed regime to shore up NABU's efforts by setting up a special anti-corruption court.
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